I have an FRPP driveshaft, blowfish shifter bracket, and a UPR billet shifter. I don't have interference problems. Also my car rides on stock springs so my rear axle is farther from the floor boards and transmission tunnel. And I have BMR motor mounts spaced a little higher so my shorty headers clear the steering shaft.
I think and hope a different shifter would solve your problems. Unfortunately I don't see a fast and easy solution for you. It's gonna be difficult if not impossible to get different measurements on all of the aftermarket shifter's out there so you can find the shortest one and then order it. Maybe you can call/email each manufacturer and ask for specs to compare and find the shortest one. Good luck with that.
Or maybe, just maybe, you can mount the transmission just a little lower by trimming the transmission mount bushing. Or raise the engine just a little bit which will lower the angle of the transmission and driveshaft. There are a few different things you can change that will hopefully fix your clearance problem.
Think about it like this. If you put the car on jackstands and let the rear axle droop like your changing the tires, I bet you solve your clearance problem. Kinda like cutting your bump stops when you install lowering springs.